Smith KA, Ball T, Conen F, Dobbie KE, Massheder J, Rey A. 2003. Exchange of greenhouse gases between soil and atmosphere: interactions of soil physical factors and biological processes. European Journal of Soil Science 54:779-791.
These authors present a broad review paper of the role of soil physical factors, mainly temperature and water-filled-pore-space, in controlling soil emissions of the greenhouse gases CO2, CH4, and N2O. The paper’s goal is stated to be to expose a variety of researchers to the links between soil physics and soil biology, as well as the importance of these fields to current research in many disciplines on global warming.
All three gases are produced and consumed in soil primarily by microorganisms, which respond to variation in soil physical parameters in different ways. In general, both temperature and WFPS impact GHG production. Higher temperatures almost always result in increased production of gases, though the Q10 values (measuring the magnitude of response to a change of 10º of temperature) vary widely in the literature for all three gases. The effect of WFPS is different, involving upper and lower bounds, though in the middle range increasing WFPS generally promotes increased gas production. Microbes are limited in their tolerance of dry conditions, such that gas production falls rapidly below some critical WFPS value; for CO2 this threshold is near 20%. WFPS is also indirectly important, through its effects on soil diffusivity. Higher WFPS as well as higher bulk density are associated with lessened CH4 oxidation, due to reduced diffusivity of both CH4 and atmospheric O2. Very high WFPS values are associated with reduction of N2O to N2, partly by limiting O2 supplies and creating larger anaerobic microsites, and partly by preventing the escape of N2O gas into rapid-diffusion pathways; it is trapped in the vicinity of microbes capable of using it as an electron acceptor.
There are other factors controlling net GHG emissions, such as the relationship between plant productivity and water table position, which will change the relationship between rates of soil organic matter oxidation to CO2 and the removal of CO2 from the atmosphere by plants; trees in particular can lower local water tables, increasing SOM oxidation while simultaneously consuming more CO2 than the previous wetland vegetation community.
I read this paper on the suggestion of my coworkers in the special topics class of fall 2010, but it applies well to the general area of my research. The reference list includes multiple interesting papers addressing particular specialties within this large topic.
Showing posts with label Introductory Chapter of PhD Thesis. Show all posts
Showing posts with label Introductory Chapter of PhD Thesis. Show all posts
Monday, September 27, 2010
Thursday, August 19, 2010
Christiansen 1979
Christiansen EA. 1979. The Wisconsinan deglaciation of southern Saskatchewan and adjacent areas. Canadian Journal of Earth Science 16: 913-938.
This author describes in considerable detail the process of deglaciation that occurred at the end of the last glacial maximum from about 17 000 years ago, as it occurs to Saskatchewan. Major geological features and patterns of melt-water drainage led to the inclusion of nearby parts of Alberta, Manitoba, Montana, and North Dakota in the analysis. Patterns during the deglaciation were identified by glacial landforms, many of which are apparent only from aerial photographs, with sample analysis in the lab including radio-carbon dating.
The period from 17 000 years to 10 000 years ago is divided into 9 phases corresponding to periods of rapid glacial retreat or temporary stasis or glacial advance. By 10 000 years ago the ice sheet that had covered nearly the entire province had retreated towards Hudson Bay and covered only a small part of the north of Saskatchewan. Glacial lakes formed from meltwater and from water flowing from the west (presumably sourced from glaciers in the Rocky mountains), sometimes reaching enormous sizes; these lakes were bordered by the glacier’s edge, and connected to each other via spillways that often carved large channels from the plains; the east-west valleys of southern Saskatchewan such as the Qu’Appelle valley are the remains of such spillways. Modern river systems such as the Saskatchewan River and the Churchill River formed during the glacial retreat, occupying low areas and spillway remnants.
The rate of deglaciation varied considerably over the studied 7 000 years, generally accelerating from about 150 m / yr to around 275 m / yr, though with frequent pauses, occasional re-advances, and variation across the glacial edge. The evidence from glacial lake-edge movements and depth patterns suggests the ice sheet melted fastest initially, but with the slowest retreat at that time indicating the sheet first thinned, and then retreated, especially around newly-uncovered Nunataks where the underlying land formed highlands.
This paper was on the suggested reading list for the course SLSC 834 in August 2010, but it is also personally interesting in describing Pleistocene events in areas I visit during Sunday drives across the center of the province.
This author describes in considerable detail the process of deglaciation that occurred at the end of the last glacial maximum from about 17 000 years ago, as it occurs to Saskatchewan. Major geological features and patterns of melt-water drainage led to the inclusion of nearby parts of Alberta, Manitoba, Montana, and North Dakota in the analysis. Patterns during the deglaciation were identified by glacial landforms, many of which are apparent only from aerial photographs, with sample analysis in the lab including radio-carbon dating.
The period from 17 000 years to 10 000 years ago is divided into 9 phases corresponding to periods of rapid glacial retreat or temporary stasis or glacial advance. By 10 000 years ago the ice sheet that had covered nearly the entire province had retreated towards Hudson Bay and covered only a small part of the north of Saskatchewan. Glacial lakes formed from meltwater and from water flowing from the west (presumably sourced from glaciers in the Rocky mountains), sometimes reaching enormous sizes; these lakes were bordered by the glacier’s edge, and connected to each other via spillways that often carved large channels from the plains; the east-west valleys of southern Saskatchewan such as the Qu’Appelle valley are the remains of such spillways. Modern river systems such as the Saskatchewan River and the Churchill River formed during the glacial retreat, occupying low areas and spillway remnants.
The rate of deglaciation varied considerably over the studied 7 000 years, generally accelerating from about 150 m / yr to around 275 m / yr, though with frequent pauses, occasional re-advances, and variation across the glacial edge. The evidence from glacial lake-edge movements and depth patterns suggests the ice sheet melted fastest initially, but with the slowest retreat at that time indicating the sheet first thinned, and then retreated, especially around newly-uncovered Nunataks where the underlying land formed highlands.
This paper was on the suggested reading list for the course SLSC 834 in August 2010, but it is also personally interesting in describing Pleistocene events in areas I visit during Sunday drives across the center of the province.
Wednesday, February 24, 2010
Siciliano et al. 2007
Siciliano SD, Ma W, Powell S. 2007. Evaluation of quantitative polymerase chain reaction to assess nosZ gene prevalence in mixed microbial communities. Canadian Journal of Microbiology 53: 636-642.
These authors examined the usefulness of qPCR in studying populations of soil bacteria, especially denitrifiers using the gene nosZ that codes for nitrous oxide reductase. This enzyme catalyzes the final reaction in the process of denitrification, converting N2O to N2. Normally, it is expressed only in severely anaerobic conditions, as it allows the use of N2O as the terminal electron acceptor during metabolism.
There are a number of factors that control the efficiency of PCR in quantitative PCR applications. The efficiency is a major component of the calculations that allow qPCR to estimate gene copy numbers in samples and thus to be used to examine population dynamics of non-culturable microorganisms from environmental samples. Of particular importance is consistency of efficiency between the amplification of the standard DNA template and the amplification of all templates in the unknown samples. Variation between the standard and the unknowns can lead to severe under- or over-estimation of target populations, while variation in efficiency between different templates within the unknown samples can lead to misestimations of relative proportions of organisms.
These authors evaluated the efficiency of qPCR in a range of experimental templates, and in a range of combinations simulating mixed populations. Little variance in efficiency was found, and this variance was not associated with genetic distance from a reference organism. The experimental design did not allow a direct examination of the influence of the geographical differences in the sources of the test sequences (Arctic, temperate-grassland, Antarctic), but this lack of association with the reference organism does indicate low or no variation among PCR efficiencies associated with some other variable.
The influence of varying PCR efficiencies among templates within a sample becomes less severe as the number of different templates rises. In a typical soil sample with perhaps 1000 different templates, no one template can utterly dominate amplification by outcompeting for primers, thus the resulting mix of amplicons at the end of 40 rounds of PCR will most likely be representative of the population mixture in the environment.
This paper is of obvious high utility to my own work, not least because the individual machine used to perform qPCR is the same individual machine that I will be using. For this and other reasons, this paper was suggested to me, repeatedly. Future reference to this paper, when I am developing my methods and when I am writing up the next paper or two, seems likely.
These authors examined the usefulness of qPCR in studying populations of soil bacteria, especially denitrifiers using the gene nosZ that codes for nitrous oxide reductase. This enzyme catalyzes the final reaction in the process of denitrification, converting N2O to N2. Normally, it is expressed only in severely anaerobic conditions, as it allows the use of N2O as the terminal electron acceptor during metabolism.
There are a number of factors that control the efficiency of PCR in quantitative PCR applications. The efficiency is a major component of the calculations that allow qPCR to estimate gene copy numbers in samples and thus to be used to examine population dynamics of non-culturable microorganisms from environmental samples. Of particular importance is consistency of efficiency between the amplification of the standard DNA template and the amplification of all templates in the unknown samples. Variation between the standard and the unknowns can lead to severe under- or over-estimation of target populations, while variation in efficiency between different templates within the unknown samples can lead to misestimations of relative proportions of organisms.
These authors evaluated the efficiency of qPCR in a range of experimental templates, and in a range of combinations simulating mixed populations. Little variance in efficiency was found, and this variance was not associated with genetic distance from a reference organism. The experimental design did not allow a direct examination of the influence of the geographical differences in the sources of the test sequences (Arctic, temperate-grassland, Antarctic), but this lack of association with the reference organism does indicate low or no variation among PCR efficiencies associated with some other variable.
The influence of varying PCR efficiencies among templates within a sample becomes less severe as the number of different templates rises. In a typical soil sample with perhaps 1000 different templates, no one template can utterly dominate amplification by outcompeting for primers, thus the resulting mix of amplicons at the end of 40 rounds of PCR will most likely be representative of the population mixture in the environment.
This paper is of obvious high utility to my own work, not least because the individual machine used to perform qPCR is the same individual machine that I will be using. For this and other reasons, this paper was suggested to me, repeatedly. Future reference to this paper, when I am developing my methods and when I am writing up the next paper or two, seems likely.
Tuesday, January 26, 2010
Conrad 1999
Conrad R. 1999. Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiology Ecology 28: 193-202.
This author reviews the chemistry behind methane production by Archaea in anaerobic environments, focusing on the contribution of H2 rather than acetate to methanogenesis. The thermodynamics and kinetics of H2-driven CH4 production are distinct from those of acetate-driven, and the stoichiometry of the situation indicates that H2 should contribute 33% of the CH4 from a given ecosystem.
Methanogenesis in anaerobic sediments and soils is the end of a short chain of microbial interactions. First, organic matter is broken down by fermenting bacteria. The products of fermentation includes H2, and the other components such as alcohols and fatty acids, are further decomposed by syntrophic bacteria, also supplying some acetate to the environment. Finally, methanogens consume either H2 and CO2 or acetate (CH3CO2-) to produce methane.
There are many studies that show this expected pattern of methanogenesis, but many other that show either over- or under-representation of H2. Where H2 contributes less CH4 than expected, the most likely explanations involve sulfate reducers, microbes capable of outcompeting H2-consuming methanogens by more efficient use of H2 and faster population growth, based on the thermodynamics of the two guilds respective metabolisms. Such situations are common in marine and acidic freshwater sediments.
Where H2 contributes more CH4 than expected, including an Antarctic soil where H2 is the basis of 100% of CH4 production, the explanation is not as well established. The explanations that have been proposed, by this and other authors, include additional sinks of acetate such as scavenging by other organisms, additional sources of H2 including geological sources, or measurements of the system taken when it was far from equilibrium. The models of H2 and CH4 dynamics are mostly based on equilibrium conditions.
That addition of sulfate inhibits methanogenesis is well established. Competition explains this observation in sediments and soils where the biological community has had time to reach something like equilibrium, with methanogens outcompeted by sulfate reducers. However, addition of sulfate to sediment immediately and completely inhibits H2-driven CH4 production, which cannot be explained by ecosystem dynamics. A model involving a threshold H2 concentration, in which H2 levels lower than some critical level determined by the thermodynamics of the situation shut down that pathway, does explain these observations.
This author reviews the chemistry behind methane production by Archaea in anaerobic environments, focusing on the contribution of H2 rather than acetate to methanogenesis. The thermodynamics and kinetics of H2-driven CH4 production are distinct from those of acetate-driven, and the stoichiometry of the situation indicates that H2 should contribute 33% of the CH4 from a given ecosystem.
Methanogenesis in anaerobic sediments and soils is the end of a short chain of microbial interactions. First, organic matter is broken down by fermenting bacteria. The products of fermentation includes H2, and the other components such as alcohols and fatty acids, are further decomposed by syntrophic bacteria, also supplying some acetate to the environment. Finally, methanogens consume either H2 and CO2 or acetate (CH3CO2-) to produce methane.
There are many studies that show this expected pattern of methanogenesis, but many other that show either over- or under-representation of H2. Where H2 contributes less CH4 than expected, the most likely explanations involve sulfate reducers, microbes capable of outcompeting H2-consuming methanogens by more efficient use of H2 and faster population growth, based on the thermodynamics of the two guilds respective metabolisms. Such situations are common in marine and acidic freshwater sediments.
Where H2 contributes more CH4 than expected, including an Antarctic soil where H2 is the basis of 100% of CH4 production, the explanation is not as well established. The explanations that have been proposed, by this and other authors, include additional sinks of acetate such as scavenging by other organisms, additional sources of H2 including geological sources, or measurements of the system taken when it was far from equilibrium. The models of H2 and CH4 dynamics are mostly based on equilibrium conditions.
That addition of sulfate inhibits methanogenesis is well established. Competition explains this observation in sediments and soils where the biological community has had time to reach something like equilibrium, with methanogens outcompeted by sulfate reducers. However, addition of sulfate to sediment immediately and completely inhibits H2-driven CH4 production, which cannot be explained by ecosystem dynamics. A model involving a threshold H2 concentration, in which H2 levels lower than some critical level determined by the thermodynamics of the situation shut down that pathway, does explain these observations.
Pennock 2004
Pennock DJ. 2004. Designing field studies in soil science. Canadian Journal of Soil Science 84: 1-10.
This author reviews the major issues surrounding field-based (as opposed to strictly laboratory-based) research, focusing on issues specific or of greatest importance to soil science. Soil science’s history could perhaps be described as a fusion of physical geography and geology with agronomy, and many published studies in the soil science journals show these roots. Following the lead of previous authors, who have included ecologists, statisticians, and philosophers and historians of science, this author divides field research into 2 major categories, broadly manipulative studies and mensurative studies. Manipulative studies are, under some definitions including one tentatively employed in this paper, the only type of study that qualify for the name “experiment”, and involve complete control over experimental conditions by the researcher. Treatments in an experiment are directly related to replication, and can be applied with great precision. Mensurative studies are those that at least partly use features of the environment beyond the control of the researcher to test hypotheses or discover new information. The key feature of a mensurative study is that the features of interest are clearly defined but not controlled (i.e. not randomized) by the person conducting the study.
Replication, and avoiding pseudoreplication, is of great importance in all types of studies. However, the replication built into a manipulative experiment in the form of repeated application of treatments is distinct from the replication of a mensurative study using repeated features of the environment. That these are different types of replication is stated in this paper, but I found no more detail or explanation than that. Pseudoreplication in this paper is discussed little in the context of independence of samples; rather the discussed risk is of attempting to draw inferences beyond the inference space of the study. This is a problem in both major types of study, and can be avoided by carefully determining and describing the inference space, and expanding that space by greater replication; too-small sample sizes are quite simply labeled as unpublishable in this paper, a sentiment I can agree with.
Determining the required sample size is a major issue for all types of studies. In this author’s presentation, this is an early step in the design of the study, after the biological and statistical questions have been established but before data collection begins. There is some discussion here as well of statistical power (the chance of avoiding a Type II error, that is of failing to reject a false null hypothesis) and recommendations of flexibility regarding especially alpha values (the chance of making a Type I error, that is of rejecting a null hypothesis that is not false). For a number of reasons, some of which are practical and logistical, alpha values larger than the ubiquitous 0.05 are encouraged, because in many cases the consequences of the 2 types of error are not even, and one may wish to concentrate on reducing the probability of a Type II error.
This paper describes 10 commonly-encountered study designs in soil science and related disciplines, and then discusses study-design concerns common to all such as replication and the need to clearly define study units, samples, populations, and other important aspects. Finally, this author presents the conclusions from all of these examples and considerations in the form of a short list of key recommendations. Quoting directly:
This author reviews the major issues surrounding field-based (as opposed to strictly laboratory-based) research, focusing on issues specific or of greatest importance to soil science. Soil science’s history could perhaps be described as a fusion of physical geography and geology with agronomy, and many published studies in the soil science journals show these roots. Following the lead of previous authors, who have included ecologists, statisticians, and philosophers and historians of science, this author divides field research into 2 major categories, broadly manipulative studies and mensurative studies. Manipulative studies are, under some definitions including one tentatively employed in this paper, the only type of study that qualify for the name “experiment”, and involve complete control over experimental conditions by the researcher. Treatments in an experiment are directly related to replication, and can be applied with great precision. Mensurative studies are those that at least partly use features of the environment beyond the control of the researcher to test hypotheses or discover new information. The key feature of a mensurative study is that the features of interest are clearly defined but not controlled (i.e. not randomized) by the person conducting the study.
Replication, and avoiding pseudoreplication, is of great importance in all types of studies. However, the replication built into a manipulative experiment in the form of repeated application of treatments is distinct from the replication of a mensurative study using repeated features of the environment. That these are different types of replication is stated in this paper, but I found no more detail or explanation than that. Pseudoreplication in this paper is discussed little in the context of independence of samples; rather the discussed risk is of attempting to draw inferences beyond the inference space of the study. This is a problem in both major types of study, and can be avoided by carefully determining and describing the inference space, and expanding that space by greater replication; too-small sample sizes are quite simply labeled as unpublishable in this paper, a sentiment I can agree with.
Determining the required sample size is a major issue for all types of studies. In this author’s presentation, this is an early step in the design of the study, after the biological and statistical questions have been established but before data collection begins. There is some discussion here as well of statistical power (the chance of avoiding a Type II error, that is of failing to reject a false null hypothesis) and recommendations of flexibility regarding especially alpha values (the chance of making a Type I error, that is of rejecting a null hypothesis that is not false). For a number of reasons, some of which are practical and logistical, alpha values larger than the ubiquitous 0.05 are encouraged, because in many cases the consequences of the 2 types of error are not even, and one may wish to concentrate on reducing the probability of a Type II error.
This paper describes 10 commonly-encountered study designs in soil science and related disciplines, and then discusses study-design concerns common to all such as replication and the need to clearly define study units, samples, populations, and other important aspects. Finally, this author presents the conclusions from all of these examples and considerations in the form of a short list of key recommendations. Quoting directly:
1. A clear definition of the research question is the initial (and most critical) step. This definition dictates the type of research design that is appropriate and the specific design issues associated with different research types.
2. The appropriateness of a given research design can be judged only after a thorough review of what is known about the research question. Exploratory pattern studies can be very informative at an early stage of research, but yield little new information for well-established research topics. Equally, the imposition of a set of treatments if little is known of the processes controlling responses is unlikely to produce comprehensive interpretations.
3. There is never a good reason for haphazard sampling – the rationale for selecting sampling points in pedological, soil geomorphic, or inventory studies should be clearly stated.
4. A clear definition of the population and the elements that comprise the population under study is very important.
5. The definition of the population dictates the extent of the study and the physical or temporal space that the results pertain to, which is critical to avoid pseudoreplication.
6. The sample support, spacing, and extent of the study must be consistent with what is known of the processes controlling the phenomena being studied.
7. The construction of hypotheses for formal testing should be based on sound physical or biological reasoning, and sufficient samples should be taken to allow reliable testing of the alternative hypotheses.
8. The exclusion of phenomena because they cannot be replicated is inherently limiting to the expansion of our knowledge of soils. Innovative approaches must continue to be developed and applied so that we can expand the scale at which field studies can be undertaken.
Wednesday, January 6, 2010
Siciliano et al. 2009
Siciliano SD, Ma WK, Ferguson S, Farrell RE. 2009. Nitrifier dominance of Arctic soil nitrous oxide emissions arises to due fungal competition with denitrifiers for nitrate. Soil Biology and Biochemistry 41: 1104-1110.
These authors examined the nitrous oxide emissions, microbial communities, and some components of nitrogen cycling in soils from three landforms at Truelove Lowland, on Devon Island. Previous results (Ma et al. 2007) had indicated that Arctic nitrous oxide emissions are not sensitive to soil moisture, at least in the range of 50% to saturated water filled pore space. This study includes a series of incubations of soil samples at a range of temperatures similar to ambient conditions, and treatments to disrupt fungi or particular types of prokaryotes.
Large differences in community composition were found between the three landforms, with the highest biomass and fungi:bacteria ratio in the wet sedge meadow and lowest in the raised beach crest (the lower foreslope was intermediate by these measures). Competition between fungi and denitrifiers for soil nitrate pools was inferred as the mechanism allowing dominance of emitted N2O by nitrifiers; fungi and denitrifiers are busy scavenging every available electron acceptor starting with nitrate and running all the way down to N2 gas, so almost any N2O that escapes was generated by nitrifiers in conditions not favoured by either of the other major groups.
This paper serves to demonstrate the very complex nature of soil biology, especially regarding the multiple and interacting pathways that may produce or consume materials of interest such as N2O. The references in this paper should be useful for digging into this complexity.
These authors examined the nitrous oxide emissions, microbial communities, and some components of nitrogen cycling in soils from three landforms at Truelove Lowland, on Devon Island. Previous results (Ma et al. 2007) had indicated that Arctic nitrous oxide emissions are not sensitive to soil moisture, at least in the range of 50% to saturated water filled pore space. This study includes a series of incubations of soil samples at a range of temperatures similar to ambient conditions, and treatments to disrupt fungi or particular types of prokaryotes.
Large differences in community composition were found between the three landforms, with the highest biomass and fungi:bacteria ratio in the wet sedge meadow and lowest in the raised beach crest (the lower foreslope was intermediate by these measures). Competition between fungi and denitrifiers for soil nitrate pools was inferred as the mechanism allowing dominance of emitted N2O by nitrifiers; fungi and denitrifiers are busy scavenging every available electron acceptor starting with nitrate and running all the way down to N2 gas, so almost any N2O that escapes was generated by nitrifiers in conditions not favoured by either of the other major groups.
This paper serves to demonstrate the very complex nature of soil biology, especially regarding the multiple and interacting pathways that may produce or consume materials of interest such as N2O. The references in this paper should be useful for digging into this complexity.
Friday, September 4, 2009
Broll et al. 1999
Broll G, Tarnocai C, Mueller G. 1999. Interactions between vegetation, nutrients and moisture in soils in the Pangnirtung Pass area, Baffin island, Canada. Permafrost and Periglacial Processes 10: 265-277.
These authors examined soils from 6 pedons in Pangnirtung Pass, a north-south pass between mountains on Cumberland Peninsula. Three pedons were from moist soils, and three from dry soils. The moisture content drove a major difference in soil structure: dry soils are not cryoturbated, resulting in strong differences in nutrient content and mineralization rates.
The goal of the study was to compare in detail these differences between dry and moist soils. This seems very similar to my PhD goals surrounding examinations of Polar Desert soils. This study thus represents a possible template for some of my own investigations.
These authors examined soils from 6 pedons in Pangnirtung Pass, a north-south pass between mountains on Cumberland Peninsula. Three pedons were from moist soils, and three from dry soils. The moisture content drove a major difference in soil structure: dry soils are not cryoturbated, resulting in strong differences in nutrient content and mineralization rates.
The goal of the study was to compare in detail these differences between dry and moist soils. This seems very similar to my PhD goals surrounding examinations of Polar Desert soils. This study thus represents a possible template for some of my own investigations.
Tuesday, August 12, 2008
Michelutti et al. 2007
Michelutti N, Douglas MSV, Smol JP. 2007. Evaluating diatom community composition in the absence of marked limnological gradients in the high Arctic: a surface sediment calibration set from Cornwallis Island (Nunavut, Canada). Polar Biology 30: 1459-1473.
These authors measured a range of water chemistry and climatological variables in a large number of lakes and ponds on and near Cornwallis Island. This island is remarkably boring in its geology, with little in the way of relief or patterns of geological variation, and provides a sort of negative control for studies of Arctic limnology and the variables exerting the strongest control on diatom species assemblages.
Overall, this study supports the hypothesis that climate and water chemistry variables are the major determinants of diatom diversity in Arctic ponds and lakes. Cornwallis’ ponds and lakes varied little in altitude, latitude, temperature, or a large number of water chemistry variables, and varied little in diatom communities, too, when compared to the existing database of Arctic limnology and diatoms.
These authors measured a range of water chemistry and climatological variables in a large number of lakes and ponds on and near Cornwallis Island. This island is remarkably boring in its geology, with little in the way of relief or patterns of geological variation, and provides a sort of negative control for studies of Arctic limnology and the variables exerting the strongest control on diatom species assemblages.
Overall, this study supports the hypothesis that climate and water chemistry variables are the major determinants of diatom diversity in Arctic ponds and lakes. Cornwallis’ ponds and lakes varied little in altitude, latitude, temperature, or a large number of water chemistry variables, and varied little in diatom communities, too, when compared to the existing database of Arctic limnology and diatoms.
Friday, August 8, 2008
Vermeij and Roopnarine 2008
Vermeij GJ, Roopnarine PD. 2008. The coming arctic invasion. Science 321: 780-781.
In this short “perspectives” article, these authors describe the historical biogeography of the North Pacific, near shore Arctic, and North Atlantic oceans, in the context of predicted patterns of climate warming over the next fifty years. In general, the climate of these areas is likely to become similar to that during the mid-Pliocene, about 3.5 million years ago. During the mid-Pliocene, large numbers of Pacific lineages of marine animals, especially molluscs, successfully colonized the Arctic ocean and established populations in the North Atlantic. While cores from the Arctic Ocean seabed suggest permanent ice-cover at the highest latitudes, there is some evidence to suggest the near shore Arctic ocean included regions that were largely ice-free. This probably resulted in much higher productivity at these locations, similar to the high productivity of the Bering Sea, and allowing large-bodied, planktotrophic animals to disperse northwards and eastwards in the generally north-east flowing currents. This pattern is expected to repeat under global warming, and because Pacific lineages are generally ecologically quite distinct from extant Atlantic species, the North Atlantic should see increased biodiversity overall. Colonization in the opposite direction, of Atlantic lineages into the North Pacific, is considered unlikely due to generally unfavourable water currents and the intensely competitive and predatory biotic environment of the Bering Sea.
In this short “perspectives” article, these authors describe the historical biogeography of the North Pacific, near shore Arctic, and North Atlantic oceans, in the context of predicted patterns of climate warming over the next fifty years. In general, the climate of these areas is likely to become similar to that during the mid-Pliocene, about 3.5 million years ago. During the mid-Pliocene, large numbers of Pacific lineages of marine animals, especially molluscs, successfully colonized the Arctic ocean and established populations in the North Atlantic. While cores from the Arctic Ocean seabed suggest permanent ice-cover at the highest latitudes, there is some evidence to suggest the near shore Arctic ocean included regions that were largely ice-free. This probably resulted in much higher productivity at these locations, similar to the high productivity of the Bering Sea, and allowing large-bodied, planktotrophic animals to disperse northwards and eastwards in the generally north-east flowing currents. This pattern is expected to repeat under global warming, and because Pacific lineages are generally ecologically quite distinct from extant Atlantic species, the North Atlantic should see increased biodiversity overall. Colonization in the opposite direction, of Atlantic lineages into the North Pacific, is considered unlikely due to generally unfavourable water currents and the intensely competitive and predatory biotic environment of the Bering Sea.
Saturday, May 17, 2008
Rodríguez-Juiz et al. 1996
Rodríguez-Juiz AM, Torrado M, Méndez J. 1996. Genome-size variation in bivalve molluscs determined by flow cytometry. Marine Biology 126: 489-497.
These authors measured nuclear DNA contents in 10 species of bivalves of commercial importance. Genome size variation in plants and poikilothermal animals had previously been associated with life-history and ecological traits, suggesting links between genome size variation and speciation events. There had been few previous studies of DNA content in molluscs. Early examples of such studies include Mirsky and Ris (1951), Hinegardner (1973, 1976), and Cavalier-Smith (1978); several earlier papers on molluscs and other poikilotherms related genome size to “specialization”, particularly the work of Hinegardner and colleagues.
Unlike most studies of DNA content, these authors included relatively large samples of each species, using 20 individuals in each species. All individuals were purchased from commercial shellfish sellers, either in Spain (9 species) or the Netherlands (Mytilus edulis), and maintained alive in the laboratory until dissection of gill tissue; the assumption that gill tissue is diploid is never stated explicitly but was used in the calculations of genome sizes. Tissue was placed in filtered, autoclaved seawater and subjected to mechanical shaking for 30 minutes; these authors do not describe in detail this shaking, is there a standard rate and magnitude of mechanical shaking of mollusc tissue? The presence of isolated cells was verified using a microscope, and cell preparations were strained through 15mm mesh and sonicated for two minutes to remove cell membranes. The nuclei were then centrifuged, resuspended in buffer that appears similar to Galbraith’s buffer (Galbraith et al. 1983), and fixed with 0.1% formaldehyde on ice. Finally, aggregations of nuclei were disrupted using a 26-gauge needle, pumped three times.
Two internal standards were employed: Capsicum annuum and chicken red blood cells (CRBCs). Isolated nuclei from these species were added to bivalve nuclei suspensions before staining, thus standards and specimens here were co-stained rather than co-prepared. The CRBCs produced a peak in the flow cytometry histograms overlapping seven of the 10 bivalve species, thus the introduction of the plant nuclei. C. annuum nuclei were employed after checking for consistent measurements with the three species of bivalves that did not overlap in peak area with CRBCs, and comparison between C. annuum and CRBCs to determine a C. annuum diploid nuclear content of 8.4 pg, larger than any bivalve measured in this study. 10 000 nuclei were measured per histogram, presumably this means total events recorded above the debris cut-off, and each specimen was measured three times.
These authors report significant intraspecific genome size variation in all 10 bivalve species. Interspecific (and between higher taxa) was much greater than intraspecific variation, but the intraspecific variation was statistically significant under 2-way ANOVA and “GSD” calculations based on the work of Gold and Amemiya (1987) and Alvarez-Fuster et al. (1991).
The discovered and possibly unexpected intraspecific variation is used to bolster an argument made in the discussion that large samples are necessary for accurate determination of genome size and genome size variation in species. This explains the difference between these results and the no-intraspecific-variation results of some previous authors that did not use large samples per species.
Following this is a discussion of Hinegardner’s (several papers in the 1970s) “specialization” assumption / hypothesis. It is described as one, then the other. These data do not support this hypothesis, which is not surprising considering how vague and taxon-specific the terms “specialized” and “generalized” are, and their underlying assumptions about species and lineage ages and rates of evolution.
These authors measured nuclear DNA contents in 10 species of bivalves of commercial importance. Genome size variation in plants and poikilothermal animals had previously been associated with life-history and ecological traits, suggesting links between genome size variation and speciation events. There had been few previous studies of DNA content in molluscs. Early examples of such studies include Mirsky and Ris (1951), Hinegardner (1973, 1976), and Cavalier-Smith (1978); several earlier papers on molluscs and other poikilotherms related genome size to “specialization”, particularly the work of Hinegardner and colleagues.
Unlike most studies of DNA content, these authors included relatively large samples of each species, using 20 individuals in each species. All individuals were purchased from commercial shellfish sellers, either in Spain (9 species) or the Netherlands (Mytilus edulis), and maintained alive in the laboratory until dissection of gill tissue; the assumption that gill tissue is diploid is never stated explicitly but was used in the calculations of genome sizes. Tissue was placed in filtered, autoclaved seawater and subjected to mechanical shaking for 30 minutes; these authors do not describe in detail this shaking, is there a standard rate and magnitude of mechanical shaking of mollusc tissue? The presence of isolated cells was verified using a microscope, and cell preparations were strained through 15mm mesh and sonicated for two minutes to remove cell membranes. The nuclei were then centrifuged, resuspended in buffer that appears similar to Galbraith’s buffer (Galbraith et al. 1983), and fixed with 0.1% formaldehyde on ice. Finally, aggregations of nuclei were disrupted using a 26-gauge needle, pumped three times.
Two internal standards were employed: Capsicum annuum and chicken red blood cells (CRBCs). Isolated nuclei from these species were added to bivalve nuclei suspensions before staining, thus standards and specimens here were co-stained rather than co-prepared. The CRBCs produced a peak in the flow cytometry histograms overlapping seven of the 10 bivalve species, thus the introduction of the plant nuclei. C. annuum nuclei were employed after checking for consistent measurements with the three species of bivalves that did not overlap in peak area with CRBCs, and comparison between C. annuum and CRBCs to determine a C. annuum diploid nuclear content of 8.4 pg, larger than any bivalve measured in this study. 10 000 nuclei were measured per histogram, presumably this means total events recorded above the debris cut-off, and each specimen was measured three times.
These authors report significant intraspecific genome size variation in all 10 bivalve species. Interspecific (and between higher taxa) was much greater than intraspecific variation, but the intraspecific variation was statistically significant under 2-way ANOVA and “GSD” calculations based on the work of Gold and Amemiya (1987) and Alvarez-Fuster et al. (1991).
The discovered and possibly unexpected intraspecific variation is used to bolster an argument made in the discussion that large samples are necessary for accurate determination of genome size and genome size variation in species. This explains the difference between these results and the no-intraspecific-variation results of some previous authors that did not use large samples per species.
Following this is a discussion of Hinegardner’s (several papers in the 1970s) “specialization” assumption / hypothesis. It is described as one, then the other. These data do not support this hypothesis, which is not surprising considering how vague and taxon-specific the terms “specialized” and “generalized” are, and their underlying assumptions about species and lineage ages and rates of evolution.
Healy and Rota 1992
Healy B, Rota E. 1992. Methods for collecting Enchytraeidae during expeditions. Soil Biology and Biochemistry 24: 1279-1281.
These authors succinctly describe methods for collecting, extracting from soil and other materials, sorting, maintaining alive, and fixing and preserving enchytraeid worms. Enchytraeids are found in all moist soils, and other materials such as tide debris and forest litter. In this study, 0.5 kg soil samples were kept in plastic bags for up to five weeks before extraction of worms.
The methods described here were developed during an expedition by the authors to north Africa; Ireland, their home, does not allow import of soil samples so they were forced to extract worms in the field. The basic extraction method is a modification of O’Connor’s (1957) “wet funnel”, which is much more clearly described and illustrated here than in that older work. Figure 1. of this paper shows a wet funnel. Worms move down away from the source of light and heat (a light bulb) into a funnel full of water connected to a bottle. After an undescribed period, probably at least three hours, the water in the bottle is dumped to Petri dishes and worms sorted. The authors describe sorting using the naked eye, but recommend a magnifying glass with attached light source for smaller specimens. Living enchytraeids can be maintained in culture with soil agar, made from 2% agar and a 1:1 mixture of soil and distilled water. Soil and debris added with the worms will ruin sterility, but provides food for the worms. Water should be added periodically to keep everything moist, about every five days. Worms in this study were narcotized with soda water, and the authors describe dilute beer as an acceptable substitute. Fixation and preservation can use “any of the usual fixatives”, though contraction of specimens can make it difficult to distinguish taxonomically-important internal organs.
These authors succinctly describe methods for collecting, extracting from soil and other materials, sorting, maintaining alive, and fixing and preserving enchytraeid worms. Enchytraeids are found in all moist soils, and other materials such as tide debris and forest litter. In this study, 0.5 kg soil samples were kept in plastic bags for up to five weeks before extraction of worms.
The methods described here were developed during an expedition by the authors to north Africa; Ireland, their home, does not allow import of soil samples so they were forced to extract worms in the field. The basic extraction method is a modification of O’Connor’s (1957) “wet funnel”, which is much more clearly described and illustrated here than in that older work. Figure 1. of this paper shows a wet funnel. Worms move down away from the source of light and heat (a light bulb) into a funnel full of water connected to a bottle. After an undescribed period, probably at least three hours, the water in the bottle is dumped to Petri dishes and worms sorted. The authors describe sorting using the naked eye, but recommend a magnifying glass with attached light source for smaller specimens. Living enchytraeids can be maintained in culture with soil agar, made from 2% agar and a 1:1 mixture of soil and distilled water. Soil and debris added with the worms will ruin sterility, but provides food for the worms. Water should be added periodically to keep everything moist, about every five days. Worms in this study were narcotized with soda water, and the authors describe dilute beer as an acceptable substitute. Fixation and preservation can use “any of the usual fixatives”, though contraction of specimens can make it difficult to distinguish taxonomically-important internal organs.
Briones et al. 2007
Briones MJI, Ineson P, Heinemeyer A. 2007. Predicting potential impacts of climate change on the geographical distribution of enchytraeids: a meta-analysis approach. Global Change Biology 13: 2252-2269.
These authors conducted a meta-analysis of all studies describing population abundances of enchytraeids. This meta-analysis required certain standards of error reporting and sample sizes for the analysis, thus many papers were not included. The authors seem inordinately enthusiastic about their meta-analysis, going to great lengths to describe both meta-analyses in general, and their own approach.
These authors focused on enchytraeids because they are often the dominant-biomass organisms of organic soils. Organic soils are not well defined in this paper, but are apparently those with very high carbon contents, thus these soils are important in the context of global climate change because changes to these systems could result in large changes in these soils’ roles as either carbon sinks or sources. Biomass of enchytraeids in organic soils can exceed 50% of all animal biomass in the soil, often dominated by one or a few species, feeding primarily on bacteria and detritus.
As an additional layer of analysis, these authors focused on one species of enchytraeid, Cognettia sphagnetorum, commonly found in European organic soils such as marshlands. The majority of studies analysed were situated in Europe, principally the UK and other parts of north-western Europe. The authors repeatedly describe this geographic bias, but do not seem otherwise concerned.
In general, high population sizes of enchytraeids were associated with Hungary (one site), alpine meadows, tropical grasslands, tropical rainforests, moorlands, moder and brown-earth soils, slightly acidic soils (pH 4 – 6), temperate rainy climates with moisture all year, and regions with moderate or cold summers. Mean annual temperature (I think that’s what the undefined acronym “MAT” stands for) higher than 16°C was strongly associated with reduced population sizes, and the loss of the focal species C. sphagnetorum. MAT higher than 10°C appears to be an inflection point, with reduced population sizes above that limit. Additionally, small population sizes were associated with warm dry summer climates (e.g. Mediterranean) and cold snowy tundra climates.
The authors present a confusing and possibly meaningless discussion of the results of their geographic analysis. They describe the range of population densities in their studies (more than 500 000 m-2 down to less than 5 000 m-2), then state these differences in mean densities were not significant under the Wilcoxon test. If the means are not different, they’re not different, so why bother to report them, except to describe the error associated with comparing across ecosystems? They ran a regression analysis using these population densities, after stating the data were not normally distributed; I do not recall how sensitive to departures from normality regression analysis may be.
The authors state that there was no association between enchytraeid population density and depth in soil, then go on to rather confusingly describe the most enchytraeid-rich soil depth horizons. Apparently, enchytraeids are generally concentrated in the top 3 to 4 cm, with very few individuals found deeper than 12 cm. Enchytraeids generally seem to require permanent high moisture levels.
The focal species apparently reproduces asexually by fragmentation; many of the studies included in the meta-analysis describe numbers of individuals that are “whole” or “regenerating”. This curious and surprising life-history trait is never referenced in this paper, seemingly treated as common knowledge among enchytraeidologists. I know of few animals that habitually reproduce this way.
Overall, I found this a confusing and disappointing paper, though I admire their attempt to reconcile a highly heterogeneous dataset. The reference list contains probably the majority of available papers on Enchytraeidae, and may be very useful in that context.
These authors conducted a meta-analysis of all studies describing population abundances of enchytraeids. This meta-analysis required certain standards of error reporting and sample sizes for the analysis, thus many papers were not included. The authors seem inordinately enthusiastic about their meta-analysis, going to great lengths to describe both meta-analyses in general, and their own approach.
These authors focused on enchytraeids because they are often the dominant-biomass organisms of organic soils. Organic soils are not well defined in this paper, but are apparently those with very high carbon contents, thus these soils are important in the context of global climate change because changes to these systems could result in large changes in these soils’ roles as either carbon sinks or sources. Biomass of enchytraeids in organic soils can exceed 50% of all animal biomass in the soil, often dominated by one or a few species, feeding primarily on bacteria and detritus.
As an additional layer of analysis, these authors focused on one species of enchytraeid, Cognettia sphagnetorum, commonly found in European organic soils such as marshlands. The majority of studies analysed were situated in Europe, principally the UK and other parts of north-western Europe. The authors repeatedly describe this geographic bias, but do not seem otherwise concerned.
In general, high population sizes of enchytraeids were associated with Hungary (one site), alpine meadows, tropical grasslands, tropical rainforests, moorlands, moder and brown-earth soils, slightly acidic soils (pH 4 – 6), temperate rainy climates with moisture all year, and regions with moderate or cold summers. Mean annual temperature (I think that’s what the undefined acronym “MAT” stands for) higher than 16°C was strongly associated with reduced population sizes, and the loss of the focal species C. sphagnetorum. MAT higher than 10°C appears to be an inflection point, with reduced population sizes above that limit. Additionally, small population sizes were associated with warm dry summer climates (e.g. Mediterranean) and cold snowy tundra climates.
The authors present a confusing and possibly meaningless discussion of the results of their geographic analysis. They describe the range of population densities in their studies (more than 500 000 m-2 down to less than 5 000 m-2), then state these differences in mean densities were not significant under the Wilcoxon test. If the means are not different, they’re not different, so why bother to report them, except to describe the error associated with comparing across ecosystems? They ran a regression analysis using these population densities, after stating the data were not normally distributed; I do not recall how sensitive to departures from normality regression analysis may be.
The authors state that there was no association between enchytraeid population density and depth in soil, then go on to rather confusingly describe the most enchytraeid-rich soil depth horizons. Apparently, enchytraeids are generally concentrated in the top 3 to 4 cm, with very few individuals found deeper than 12 cm. Enchytraeids generally seem to require permanent high moisture levels.
The focal species apparently reproduces asexually by fragmentation; many of the studies included in the meta-analysis describe numbers of individuals that are “whole” or “regenerating”. This curious and surprising life-history trait is never referenced in this paper, seemingly treated as common knowledge among enchytraeidologists. I know of few animals that habitually reproduce this way.
Overall, I found this a confusing and disappointing paper, though I admire their attempt to reconcile a highly heterogeneous dataset. The reference list contains probably the majority of available papers on Enchytraeidae, and may be very useful in that context.
Friday, May 9, 2008
Bajer et al. 1961
Bajer A, Hansen-Melander E, Melander Y, Molè-Bajer J. 1961. Meiosis in Cepaea nemoralis studied by microcinematography. Chromosoma (Berl.) 12: 374-381.
These authors studied spermatogenesis in the helicid land snail Cepaea nemoralis, an hermaphrodite with accessible meiotic cells containing 28 bivalents. The stated aim of this paper is to contribute to knowledge of basic meiotic processes in animals, and compare them to meiosis in plants. This was accomplished through the use of an apparently cutting-edge-technology phase-contrast microscope, and for at least this paper, 16mm film.
Most of this paper is a description of the changes in shape and size of the nucleus of meiotic cells, and the movements of the chromosomes in the minutes immediately before and after the disappearance of the nuclear membrane. The nucleus is apparently somewhat unstable during prophase, changing position in the cell in a random fashion and changing shape rapidly. The chromosomes inside the intact nucleus also seem to move randomly, in a manner that does not suggest pulling by microtubules or other cytoskeletal components. Just prior to the disappearance of the nuclear membrane, the nucleus increases in size; this phenomenon is not explained even by speculation in this paper.
Previous work by these authors, using the same microscope, included measurements of nucleus mass by interference microscopy. How mass is measured is not clearly explained, but this paper is the first reference to this measurement I have seen.
These authors studied spermatogenesis in the helicid land snail Cepaea nemoralis, an hermaphrodite with accessible meiotic cells containing 28 bivalents. The stated aim of this paper is to contribute to knowledge of basic meiotic processes in animals, and compare them to meiosis in plants. This was accomplished through the use of an apparently cutting-edge-technology phase-contrast microscope, and for at least this paper, 16mm film.
Most of this paper is a description of the changes in shape and size of the nucleus of meiotic cells, and the movements of the chromosomes in the minutes immediately before and after the disappearance of the nuclear membrane. The nucleus is apparently somewhat unstable during prophase, changing position in the cell in a random fashion and changing shape rapidly. The chromosomes inside the intact nucleus also seem to move randomly, in a manner that does not suggest pulling by microtubules or other cytoskeletal components. Just prior to the disappearance of the nuclear membrane, the nucleus increases in size; this phenomenon is not explained even by speculation in this paper.
Previous work by these authors, using the same microscope, included measurements of nucleus mass by interference microscopy. How mass is measured is not clearly explained, but this paper is the first reference to this measurement I have seen.
Wednesday, April 30, 2008
Olsson 1981
Olsson TI. 1981. Overwintering of benthic macroinvertebrates in ice and frozen sediment in a North Swedish river. Holarctic Ecology 4: 161-166.
This author examined freezing tolerance and freezing resistance in some river-dwelling invertebrates in the Arctic. The study river is one of the few in northern Sweden that has not been dammed for hydroelectric purposes, allowing water levels to fluctuate through a wide range. Ice thickness in winter can exceed 50 cm, and the shallow littoral zone of the river freezes several centimetres into the sediment. Water level is lowest in winter, freezing sediments that are under as much as 4m of flowing water in summer. Spring thaw may occur bottom-to-top in shallow areas, as sunlight penetrates ice and heats underlying sediment, which thaws under a layer of ice; this slow thawing in sediments may be important for winter and spring survival of invertebrates and plants.
Ice and sediment cores taken from the river edge in winter included a range of frozen invertebrates. These animals were returned to the lab and allowed to thaw, to estimate winter survival. Most animals had very high survivorship; one major exception was the isopod Asellus aquaticus, found in a single aggregration of nearly 500 individuals, most of whom were dead upon thawing.
Winter survival was also estimated by freezing some animals in the lab, maintaining them frozen for several months, and thawing. Mechanical damage was inferred to be more severe in the lab than under field conditions as animals without shells or hard cases (e.g. gastropods, trichoptera larvae) such as oligochaetes suffered very high mortalities in the lab, but high survivorship in the field. This author is careful to note that lab freezing conditions included natural sediments and plants, as it has previously been shown that simple freezing of open water (e.g. in a bucket) is lethal to even the most cold-tolerant species, probably due to the mechanical damage incurred by expanding ice crystals that can be avoided by shelter among sediments or plant tissues.
Several cold and freezing putative adaptations were discovered, including the formation of epiphragms in some gastropods, a thin closure of the shell apeture not previously observed in aquatic snails, but common among dessication-resistant land snails. Some trichopteran larvae were found to have blocked their cases, though they were not pupal or prepupal. This blockage may have served to prevent ice formation and associated mechanical damage inside the cases. Some species were found in summer collections but were absent from frozen cores, including gammarid amphipods, suggesting winter migration to unfrozen deeper portions of the river.
This author examined freezing tolerance and freezing resistance in some river-dwelling invertebrates in the Arctic. The study river is one of the few in northern Sweden that has not been dammed for hydroelectric purposes, allowing water levels to fluctuate through a wide range. Ice thickness in winter can exceed 50 cm, and the shallow littoral zone of the river freezes several centimetres into the sediment. Water level is lowest in winter, freezing sediments that are under as much as 4m of flowing water in summer. Spring thaw may occur bottom-to-top in shallow areas, as sunlight penetrates ice and heats underlying sediment, which thaws under a layer of ice; this slow thawing in sediments may be important for winter and spring survival of invertebrates and plants.
Ice and sediment cores taken from the river edge in winter included a range of frozen invertebrates. These animals were returned to the lab and allowed to thaw, to estimate winter survival. Most animals had very high survivorship; one major exception was the isopod Asellus aquaticus, found in a single aggregration of nearly 500 individuals, most of whom were dead upon thawing.
Winter survival was also estimated by freezing some animals in the lab, maintaining them frozen for several months, and thawing. Mechanical damage was inferred to be more severe in the lab than under field conditions as animals without shells or hard cases (e.g. gastropods, trichoptera larvae) such as oligochaetes suffered very high mortalities in the lab, but high survivorship in the field. This author is careful to note that lab freezing conditions included natural sediments and plants, as it has previously been shown that simple freezing of open water (e.g. in a bucket) is lethal to even the most cold-tolerant species, probably due to the mechanical damage incurred by expanding ice crystals that can be avoided by shelter among sediments or plant tissues.
Several cold and freezing putative adaptations were discovered, including the formation of epiphragms in some gastropods, a thin closure of the shell apeture not previously observed in aquatic snails, but common among dessication-resistant land snails. Some trichopteran larvae were found to have blocked their cases, though they were not pupal or prepupal. This blockage may have served to prevent ice formation and associated mechanical damage inside the cases. Some species were found in summer collections but were absent from frozen cores, including gammarid amphipods, suggesting winter migration to unfrozen deeper portions of the river.
Milner 1994
Milner AM. 1994. Colonization and succession of invertebrate communities in a new stream in Glacier Bay National Park, Alaska. Freshwater Biology 32: 387-400.
This author describes long term monitoring of colonization and succession in a stream recently formed from a retreating glacier in south-eastern Alaska. The glacier filled its bay around 1700 AD, and has been retreating since, forming new streams and lakes, and novel habitats similar to what is thought to have occurred across northern North America and Eurasia at the end of the last ice age. There are few previous studies of stream systems that completely lack an upstream source of drift-colonizing organisms; this author describes this work as unique regarding its long time frame (12 years), spatial extent (kilometres), and primary succession characteristics.
Of the possible routes for colonization of the study stream by invertebrates, only aerial oviposition is possible as the other routes rely on suitable habitat upstream or downstream of the study site. The study site is bounded by the ocean below, and a new proglacial lake and associated ice field above. The first organisms present in the stream were chironomids, of species known to be exceptionally tolerant of cold water (~2°C). Species richness increased through the study period, with the addition of one species of Ephemeroptera, one species of Plecoptera, and a turnover in chironomid species and relative abundances.
A portion of the discussion section describes the distinction between fugitive species, good dispersers but poor competitors with habitat refugia in extreme environments, and opportunistic species, good dispersers that are also good competitors in their local microhabitats, maintained by disturbance. The first few chironomid species found in the stream are considered fugitive species because their population abundances were severely reduced in later years as other species, including a predatory stonefly, became established. A later portion discusses deterministic and stochastic processes in succession, arguing that water temperature and flow characteristics have been strong deterministic drivers of this stream system, in contrast to the strong role argued for stochastic processes (‘first come first served’) in other, more temperate streams studied by other authors.
The distinctions between fugitives and opportunists, and between stochastic and deterministic, would not be possible without species-level identification of chironomid larvae. Several species are described as Genus sp. A or similar, but nonetheless the ability to discriminate between closely related species with different ecological characteristics is clearly applied, allowing levels of analysis not normally seen in stream-succession studies.
This paper is part of a special issue of the journal Freshwater Biology, devoted to alpine and polar freshwater environments, and seems to be slightly lower in scientific rigour compared to normal papers in this journal. Many of the citations in this paper are of the author’s own previous unpublished data, and key blocks of data such as particular field collection seasons, have already been described in previous publications; this paper apparently serves primarily to integrate across the long time frame of repeated sampling.
This author describes long term monitoring of colonization and succession in a stream recently formed from a retreating glacier in south-eastern Alaska. The glacier filled its bay around 1700 AD, and has been retreating since, forming new streams and lakes, and novel habitats similar to what is thought to have occurred across northern North America and Eurasia at the end of the last ice age. There are few previous studies of stream systems that completely lack an upstream source of drift-colonizing organisms; this author describes this work as unique regarding its long time frame (12 years), spatial extent (kilometres), and primary succession characteristics.
Of the possible routes for colonization of the study stream by invertebrates, only aerial oviposition is possible as the other routes rely on suitable habitat upstream or downstream of the study site. The study site is bounded by the ocean below, and a new proglacial lake and associated ice field above. The first organisms present in the stream were chironomids, of species known to be exceptionally tolerant of cold water (~2°C). Species richness increased through the study period, with the addition of one species of Ephemeroptera, one species of Plecoptera, and a turnover in chironomid species and relative abundances.
A portion of the discussion section describes the distinction between fugitive species, good dispersers but poor competitors with habitat refugia in extreme environments, and opportunistic species, good dispersers that are also good competitors in their local microhabitats, maintained by disturbance. The first few chironomid species found in the stream are considered fugitive species because their population abundances were severely reduced in later years as other species, including a predatory stonefly, became established. A later portion discusses deterministic and stochastic processes in succession, arguing that water temperature and flow characteristics have been strong deterministic drivers of this stream system, in contrast to the strong role argued for stochastic processes (‘first come first served’) in other, more temperate streams studied by other authors.
The distinctions between fugitives and opportunists, and between stochastic and deterministic, would not be possible without species-level identification of chironomid larvae. Several species are described as Genus sp. A or similar, but nonetheless the ability to discriminate between closely related species with different ecological characteristics is clearly applied, allowing levels of analysis not normally seen in stream-succession studies.
This paper is part of a special issue of the journal Freshwater Biology, devoted to alpine and polar freshwater environments, and seems to be slightly lower in scientific rigour compared to normal papers in this journal. Many of the citations in this paper are of the author’s own previous unpublished data, and key blocks of data such as particular field collection seasons, have already been described in previous publications; this paper apparently serves primarily to integrate across the long time frame of repeated sampling.
Tuesday, April 22, 2008
Murkin et al. 1983
Murkin HR, Abbott PG, Kadlec JA. 1983. A comparison of activity traps and sweep nets for sampling nektonic invertebrates in wetlands. Freshwater Invertebrate Biology 2: 99-106.
These authors compared a specific activity trap design to a specific sweep net technique for sampling nektonic animals in small ponds in a wetland in Manitoba, in the context of evaluating incorporation of these techniques into long-term wetlands ecology monitoring programs. The activity trap consists of a 3.8 L glass bottle with a plast funnel inserted in the opening, held together with wire and elastic bands, and suspended in the water column from a stake driven at an angle into the sediment. The sweep net technique avoids benthic organisms and most benthic debris and vegetation by sweeping vertically upwards from resting flat on the substrate.
The fauna collected by the two methods was correlated when measured across variables of water temperature and water depth, suggesting that for at least total diversity, the two methods are collecting similar samples. Differences emerged when fish and predatory invertebrates were present in the traps, possibly attracted to the traps by the presence of prey species, including Hyalella azteca, which may have been subsequently consummed. Fish and other fast-moving animals were also rarely collected by the sweep nets. Activity traps appeared to select for the most mobile size- and age-classes of gastropods such as lymnaeids, which were absent from most sweep net samples.
The activity traps provide quantitative samples of only some taxa, primarily those that were classified as “herbivore-detritivores” in the absence of predators inside the traps. Predatory taxa were probably overrepresented in the traps, while some apparent prey taxa were underrepresented in traps when predators were present.
The activity traps provided several important advantages compared to sweep nets. There is reduced inter-operator variation, traps were easier to use among vegetation, they collected even fast-moving animals such as fish and large predatory invertebrates, and they integrated the nekton over 24 hours, unlike the time-of-day specific sweep nets.
These authors compared a specific activity trap design to a specific sweep net technique for sampling nektonic animals in small ponds in a wetland in Manitoba, in the context of evaluating incorporation of these techniques into long-term wetlands ecology monitoring programs. The activity trap consists of a 3.8 L glass bottle with a plast funnel inserted in the opening, held together with wire and elastic bands, and suspended in the water column from a stake driven at an angle into the sediment. The sweep net technique avoids benthic organisms and most benthic debris and vegetation by sweeping vertically upwards from resting flat on the substrate.
The fauna collected by the two methods was correlated when measured across variables of water temperature and water depth, suggesting that for at least total diversity, the two methods are collecting similar samples. Differences emerged when fish and predatory invertebrates were present in the traps, possibly attracted to the traps by the presence of prey species, including Hyalella azteca, which may have been subsequently consummed. Fish and other fast-moving animals were also rarely collected by the sweep nets. Activity traps appeared to select for the most mobile size- and age-classes of gastropods such as lymnaeids, which were absent from most sweep net samples.
The activity traps provide quantitative samples of only some taxa, primarily those that were classified as “herbivore-detritivores” in the absence of predators inside the traps. Predatory taxa were probably overrepresented in the traps, while some apparent prey taxa were underrepresented in traps when predators were present.
The activity traps provided several important advantages compared to sweep nets. There is reduced inter-operator variation, traps were easier to use among vegetation, they collected even fast-moving animals such as fish and large predatory invertebrates, and they integrated the nekton over 24 hours, unlike the time-of-day specific sweep nets.
Wednesday, April 9, 2008
Witt and Hebert 2000
Witt JDS, Hebert PDN. 2000. Cryptic species diversity and evolution in the amphipod genus Hyalella within central glaciated North America: a molecular phylogenetic approach. Canadian Journal of Fisheries and Aquatic Sciences 57: 687-698.
These authors examined mtDNA and nuclear (allozyme) markers in a species of amphipod that is a strong candidate for cryptic diversification. Hyalella azteca has a vast geographic range, stretching from Panama to north of the Arctic circle and from the Atlantic to Pacific coasts of North America. It is found in a wide range of different freshwater habitats, including streams, rivers, ponds and lakes up to and including the Laurentian Great Lakes. These freshwater habitats are also highly disjunct in geographic distribution. All of these factors together present the large number of populations of this species with a huge range of selective pressures and long times since many populations last were in contact.
The goals of this study were first to extend earlier work that was suggestive of diversity within this putative species, and second to determine the ages of lineages with Hyalella azteca and compare those ages with major geological events such as the Pleistocene glaciations and the formation of the Isthmus of Panama. The subgenus, Hyalella, to which H. azteca belongs was previously thought to have originated after the formation of the Isthmus, by colonization from the genus’ center of origin in South America.
Seven mtDNA lineages were detected that differed from each other by between 9 and 28% at the gene COI. This exceeds many divergence values between congeneric or occasionally confamilial species. These authors recommend that these seven lineages be considered cryptic species, based on this and some of the biogeographic distribution evidence, and furthermore suggest that Clade 7, apparently divergent also in morphology, be included in the species Hyalella inermis, a taxon that was included into H. azteca early in the 20th century but should be resurrected.
Patterns of allozyme differences within Clade 5 and Clade 6 were consistent with a scenario of divergence during isolation in distinct glacial refugia during the Pleistocene. Other patterns of divergence strongly suggest the subgenus originated long before the Isthmus of Panama formed. These authors estimated a divergence date for the subgenus of 11 million years ago, while the Isthmus formed approximately 3 million years ago.
From a practical point of view, this paper is very important to me. First, it provides an example of a comparison of phylogeographic patterns with major geological events and inferred patterns of dispersal and colonization. Second, many of the collection locations described in this paper are near my proposed route of collection and travel from Guelph to Winnipeg, planned for the summer of 2008. As I intend to collect specimens of Hyalella azteca (or, indeed, of species within this apparent species complex), recollections from some of the same locations as this study are desirable.
These authors examined mtDNA and nuclear (allozyme) markers in a species of amphipod that is a strong candidate for cryptic diversification. Hyalella azteca has a vast geographic range, stretching from Panama to north of the Arctic circle and from the Atlantic to Pacific coasts of North America. It is found in a wide range of different freshwater habitats, including streams, rivers, ponds and lakes up to and including the Laurentian Great Lakes. These freshwater habitats are also highly disjunct in geographic distribution. All of these factors together present the large number of populations of this species with a huge range of selective pressures and long times since many populations last were in contact.
The goals of this study were first to extend earlier work that was suggestive of diversity within this putative species, and second to determine the ages of lineages with Hyalella azteca and compare those ages with major geological events such as the Pleistocene glaciations and the formation of the Isthmus of Panama. The subgenus, Hyalella, to which H. azteca belongs was previously thought to have originated after the formation of the Isthmus, by colonization from the genus’ center of origin in South America.
Seven mtDNA lineages were detected that differed from each other by between 9 and 28% at the gene COI. This exceeds many divergence values between congeneric or occasionally confamilial species. These authors recommend that these seven lineages be considered cryptic species, based on this and some of the biogeographic distribution evidence, and furthermore suggest that Clade 7, apparently divergent also in morphology, be included in the species Hyalella inermis, a taxon that was included into H. azteca early in the 20th century but should be resurrected.
Patterns of allozyme differences within Clade 5 and Clade 6 were consistent with a scenario of divergence during isolation in distinct glacial refugia during the Pleistocene. Other patterns of divergence strongly suggest the subgenus originated long before the Isthmus of Panama formed. These authors estimated a divergence date for the subgenus of 11 million years ago, while the Isthmus formed approximately 3 million years ago.
From a practical point of view, this paper is very important to me. First, it provides an example of a comparison of phylogeographic patterns with major geological events and inferred patterns of dispersal and colonization. Second, many of the collection locations described in this paper are near my proposed route of collection and travel from Guelph to Winnipeg, planned for the summer of 2008. As I intend to collect specimens of Hyalella azteca (or, indeed, of species within this apparent species complex), recollections from some of the same locations as this study are desirable.
Tuesday, April 8, 2008
Stewart and Dillon 2004
Stewart TW, Dillon RT Jr. 2004. Species composition and geographic distribution of Virginia’s freshwater gastropod fauna: a review using historical records. American Malacological Bulletin 19: 79-91.
These authors reviewed museum collections, electronic databases, and published and unpublished reports of freshwater gastropod species occurring in Virginia. More than 50 species were found in the state, with a few species records only from many decades previously suggesting possible extinction or extirpation. The habitats and some tolerances of some species were also described, especially for particularly abundant species and a few rare species restricted to small areas such as cave systems. This constitutes the first comprehensive review of Virginia’s freshwater Gastropoda in 30 years. The authors end the paper by suggesting it be used to further conservation efforts in the state.
These authors reviewed museum collections, electronic databases, and published and unpublished reports of freshwater gastropod species occurring in Virginia. More than 50 species were found in the state, with a few species records only from many decades previously suggesting possible extinction or extirpation. The habitats and some tolerances of some species were also described, especially for particularly abundant species and a few rare species restricted to small areas such as cave systems. This constitutes the first comprehensive review of Virginia’s freshwater Gastropoda in 30 years. The authors end the paper by suggesting it be used to further conservation efforts in the state.
Monday, April 7, 2008
Rhode 1996
Rhode K. 1996. Rapoport’s Rule is a local phenomenon and cannot explain latitudinal gradients in species diversity. Biodiversity Letters 3: 10-13.
This author summarizes current evidence for Rapoport’s Rule, here defined as a gradient of increasing species latitudinal ranges with increasing latitude. The studies cited fall into one of two categories: either they support the existence of Rapoport’s Rule, but only in the northern hemisphere, in terrestrial or freshwater environments north of approximately 40°N, or they did not find evidence in support of Rapoport’s Rule and studied organisms living in the tropics, the southern hemisphere, and/or marine environments. The landmasses north of 40°N are roughly coincident with the extent of the glaciation of the Pleistocene, suggesting that Rapoport’s Rule may be more a result of historical processes than current ecological conditions.
Much of the paper is a direct critique of Stevens (1989, 1996), who (in 1996) attempts to extend the generality of Rapoport’s Rule to marine teleosts and depth. According to Rhode (1996), Stevens (1989, 1996) neglects to consider two important potentially confounding effects. First, sampling bias alone (as described by Colwell & Hurtt, 1994) can lead to an apparent Rapoport’s Effect as per-species sampling effort will decrease with increasing species richness if total sampling effort is held constant, and the species in the more species rich region will appear to have smaller ranges. Second, Stevens (1989, 1996) used means of species ranges (latitudinal, depth, or altitude), but the mean is a poor measure of central tendency in this context (as pointed out by Roy et al., 1994) because of the strongly non-normal distributions of species ranges. Additionally, Rhode (1996) states that high-latitude marine fishes experience less temperature variation with depth than do tropical species, so cannot be considered to have broader temperature tolerances.
This paper clarifies some of the debate apparent in the literature extending to 2008 (e.g. Krasnov et al. 2008), but I am left with some suspicions about Rhode’s (1996) fact-checking. Besides some odd typos in the literature cited section, Rhode (1996) describes France (1992) as finding a Rapoport’s Rule pattern in North American freshwater crayfish and amphipods north of approximately 40°N. However, France (1992) includes data about crayfish and amphipod species ranges from approximately 30°N, which I do not consider equivalent to “approximately 40°N”. France (1992) also includes relevant data about other groups, molluscs, mammals, “herps”, and “fishes” derived from Stevens (1989). In short, this paper opens as many questions about the status of the debate in the biogeographical literature about Rapoport’s Rule as it answers.
This author summarizes current evidence for Rapoport’s Rule, here defined as a gradient of increasing species latitudinal ranges with increasing latitude. The studies cited fall into one of two categories: either they support the existence of Rapoport’s Rule, but only in the northern hemisphere, in terrestrial or freshwater environments north of approximately 40°N, or they did not find evidence in support of Rapoport’s Rule and studied organisms living in the tropics, the southern hemisphere, and/or marine environments. The landmasses north of 40°N are roughly coincident with the extent of the glaciation of the Pleistocene, suggesting that Rapoport’s Rule may be more a result of historical processes than current ecological conditions.
Much of the paper is a direct critique of Stevens (1989, 1996), who (in 1996) attempts to extend the generality of Rapoport’s Rule to marine teleosts and depth. According to Rhode (1996), Stevens (1989, 1996) neglects to consider two important potentially confounding effects. First, sampling bias alone (as described by Colwell & Hurtt, 1994) can lead to an apparent Rapoport’s Effect as per-species sampling effort will decrease with increasing species richness if total sampling effort is held constant, and the species in the more species rich region will appear to have smaller ranges. Second, Stevens (1989, 1996) used means of species ranges (latitudinal, depth, or altitude), but the mean is a poor measure of central tendency in this context (as pointed out by Roy et al., 1994) because of the strongly non-normal distributions of species ranges. Additionally, Rhode (1996) states that high-latitude marine fishes experience less temperature variation with depth than do tropical species, so cannot be considered to have broader temperature tolerances.
This paper clarifies some of the debate apparent in the literature extending to 2008 (e.g. Krasnov et al. 2008), but I am left with some suspicions about Rhode’s (1996) fact-checking. Besides some odd typos in the literature cited section, Rhode (1996) describes France (1992) as finding a Rapoport’s Rule pattern in North American freshwater crayfish and amphipods north of approximately 40°N. However, France (1992) includes data about crayfish and amphipod species ranges from approximately 30°N, which I do not consider equivalent to “approximately 40°N”. France (1992) also includes relevant data about other groups, molluscs, mammals, “herps”, and “fishes” derived from Stevens (1989). In short, this paper opens as many questions about the status of the debate in the biogeographical literature about Rapoport’s Rule as it answers.
Chapin and Körner 1994
Chapin FS III, Körner C. 1994. Arctic and alpine biodiversity: patterns, causes and ecosystem consequences. Trends in Ecology and Evolution 9: 45-47.
These authors summarize the major points discussed at a meeting in Norway of researchers studying Arctic and alpine ecosystems, in the context of climate change and 14 major biomes. No published works are cited in this paper, rather several prominent researchers are mentioned as contributing various components of the meeting.
Arctic and alpine ecosystems were grouped together and described as “critical” for five reasons: 1. High latitudes are expected to experience the most change in climate; 2. The ecological consequences of warming will be most severe in cold regions; 3. High altitudes with low atmospheric pressures are expected to be most limiting for CO2 and consequently will respond strongly to changes in CO2 concentrations; 4. Arctic systems include large pools of frozen carbon and methane, and will thus generate important feedback effects during warming; 5. Arctic and alpine ecosystems are relatively simple systems and may show clear effects on species of ecosystem processes. Point 5 is probably most directly applicable to my own work, in that it reinforces the utility of low-species-richness and extreme-climate environments for examinations of interactions between abiotic factors and evolutionary processes.
Much of the discussion centres on the Arctic and alpine flora, which show patterns of diversity strongly associated with historical forces such as the Pleistocene glaciations. Arctic floras tend to be broadly distributed, often holarctic, while most alpine systems are more specific to small areas. In general, stable Arctic and alpine systems show diversity curves that fit the geometric model, suggesting that competitive interactions for limiting resources best explain patterns of diversity, rather than abiotic factors.
In contrast, animal diversity shows a clear latitudinal and altitudinal gradient, with associated patterns of taxonomic replacement. For example, coleopteran species richness declines with latitude while dipteran species richness increases.
The processes that humans are most interested in for economic and other reasons are those most sensitive to species composition, such as pollination and trophic dynamics. Other processes are much less sensitive to species composition within functional groups, for example many biogeochemistry processes.
In summary, the described conference demonstrated that a great deal is known about patterns of biodiversity in Arctic and alpine ecosystems as well as globally. These patterns appear to have important consequences for ecosystem function, and further research is urged in refining knowledge of species diversity patterns to better detect changes due to climate, experimental manipulations simulating changes in climate and CO2, and simulation modelling of long-term and large-scale processes.
These authors summarize the major points discussed at a meeting in Norway of researchers studying Arctic and alpine ecosystems, in the context of climate change and 14 major biomes. No published works are cited in this paper, rather several prominent researchers are mentioned as contributing various components of the meeting.
Arctic and alpine ecosystems were grouped together and described as “critical” for five reasons: 1. High latitudes are expected to experience the most change in climate; 2. The ecological consequences of warming will be most severe in cold regions; 3. High altitudes with low atmospheric pressures are expected to be most limiting for CO2 and consequently will respond strongly to changes in CO2 concentrations; 4. Arctic systems include large pools of frozen carbon and methane, and will thus generate important feedback effects during warming; 5. Arctic and alpine ecosystems are relatively simple systems and may show clear effects on species of ecosystem processes. Point 5 is probably most directly applicable to my own work, in that it reinforces the utility of low-species-richness and extreme-climate environments for examinations of interactions between abiotic factors and evolutionary processes.
Much of the discussion centres on the Arctic and alpine flora, which show patterns of diversity strongly associated with historical forces such as the Pleistocene glaciations. Arctic floras tend to be broadly distributed, often holarctic, while most alpine systems are more specific to small areas. In general, stable Arctic and alpine systems show diversity curves that fit the geometric model, suggesting that competitive interactions for limiting resources best explain patterns of diversity, rather than abiotic factors.
In contrast, animal diversity shows a clear latitudinal and altitudinal gradient, with associated patterns of taxonomic replacement. For example, coleopteran species richness declines with latitude while dipteran species richness increases.
The processes that humans are most interested in for economic and other reasons are those most sensitive to species composition, such as pollination and trophic dynamics. Other processes are much less sensitive to species composition within functional groups, for example many biogeochemistry processes.
In summary, the described conference demonstrated that a great deal is known about patterns of biodiversity in Arctic and alpine ecosystems as well as globally. These patterns appear to have important consequences for ecosystem function, and further research is urged in refining knowledge of species diversity patterns to better detect changes due to climate, experimental manipulations simulating changes in climate and CO2, and simulation modelling of long-term and large-scale processes.
Subscribe to:
Posts (Atom)
